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67 results for “potassium channel”
Input files for simulation of potassium channels using the AMOEBA polarizable force field
<p>This dataset contains input Tinker xyz and key files for the simulation of KcsA potassium channels in DOPC bilayer, a simple script for converting CHARMM pdb file to Tinker xyz file, and modified Tinker source code to support one-dimensional position restraints.<br> "params.tar.gz" contains a description of the force field modifications.<br> <br> To use "mod2", add the following lines to the key file.</p> <pre><code>#compatible with amoebabio18.prm polarize 5 1.4500 0.3900 3 polarize 11 1.4500 0.3900 9 polarize 3 1.7500 0.3900 1 5 7 50 225 227 polarize 9 1.7500 0.3900 1 7 11 50 225 227</code></pre> <p> </p>
Noncanonical electromechanical coupling paths in cardiac hERG potassium channel (semi-binary contact maps)
<p>Matrices of the semi-binary contact maps of the following open and closed systems: WT, A527L, A614G, L524R, L529H, L532H, T425L, T618L, W563L.</p> <p>The residue numbering is not the official one because the first residues (397) of hERG (PAS domain) were not included in our simulations so that each subunit comprizes 466 residues. Moreover, the four subunits were numbered consecutively. The official numbering of a residue can be easily recovered. The general rule is:</p> <p>official residue - 397 = our residue</p> <p>For example, the official T425 corresponds to T28 in the first subunit (425-397), T494 in the second subunit (425-397+466), T960 in the third subunit (425-397+466+466), and T1426 in the fourth subunit (425-397+466+466+466).</p>
Molecular Dynamics Simulations of Hydrophilic (QTY) Potassium Ion Channels in Water
<p>You can find here the molecular dynamics (MD) trajectories of QTY proteins in water performed for the "Computational engineering of water-soluble potassium ion channels through QTY transformation" manuscript. Please cite our paper and the previous Zenodo dataset when referring to or using this data. If you have any questions, please contact me (Eva Smorodina) at ribes.ev@gmail.com. Thank you!<br><br>Smorodina, E. (2024). Molecular Dynamics Simulations of Hydrophobic (cryo-EM and Native) and Hydrophilic (QTY) Potassium Ion Channels [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10592842</p>
dataset relate to article: "Functional Characterization of Two Variants at the Intron 6-Exon 7 Boundary of the KCNQ2 Potassium Channel Gene Causing Distinct Epileptic Phenotypes"
<p><strong>Sequencing Analysis performed at Fondazione Besta and carried out as part of the study mentioned at title</strong></p>
A selective small-molecule agonist of G protein-gated inwardly-rectifying potassium channels reduces epileptiform activity in a mouse model of tumor associated epilepsy - Thy1-GCaMP Tumor Electrophysiology
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Discovery of a potent, Kv7.3-selective potassium channel opener from a Polynesian traditional botanical anticonvulsant
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The potassium channel subunit Kv1.8 (Kcna10) is essential for the distinctive outwardly rectifying conductances of type I and II vestibular hair cells
<p>In amniotes, head motions and tilt are detected by two types of vestibular hair cells (HCs) with strikingly different morphology and physiology. Mature type I HCs express a large and very unusual potassium conductance, g<sub>K,L</sub>, which activates negative to resting potential, confers very negative resting potentials and low input resistances, and enhances an unusual non-quantal transmission from type I cells onto their calyceal afferent terminals. Following clues pointing to K<sub>V</sub>1.8 (KCNA10) in the Shaker K channel family as a candidate g<sub>K,L</sub> subunit, we compared whole-cell voltage-dependent currents from utricular hair cells of K<sub>V</sub>1.8-null mice and littermate controls. We found that K<sub>V</sub>1.8 is necessary not just for g<sub>K,L</sub> but also for fast-inactivating and delayed rectifier currents in type II HCs, which activate positive to resting potential. The distinct properties of the three K<sub>V</sub>1.8-dependent conductances may reflect different mixing with other K<sub>V</sub>1 subunits, such as K<sub>V</sub>1.4 (KCNA4). In K<sub>V</sub>1.8-null HCs of both types, residual outwardly rectifying conductances include K<sub>V</sub>7 (KCNQ) channels. </p> <p>Current clamp records show that in both HC types, K<sub>V</sub>1.8-dependent conductances increase the speed and damping of voltage responses. Features that speed up vestibular receptor potentials and non-quantal afferent transmission may have helped stabilize locomotion as tetrapods moved from water to land.</p>
Square Antiprismatic Ion Chelation Is a Key Determinant for Potassium Channel Selectivity
<p>Files presented here are archives K_DB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz.</p> <p>Archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz contain models of indentified sites for potassium channels (dataset #1), other membrane proteins, excluding potassium channels (dataset #2) and non-membrane proteins form PDB70 (dataset #3). The name of a folder in the dataset corresponds to PDB ID of a protein for which calculation were made. Each folder contain the following files:</p> <ul> <li><PDB_ID>.pdb — the original pdb file.</li> <li><PDB_ID>.ref — file that contains oxygens and nitrogens from original pdb that were used for scanning.</li> <li><PDB_ID>_COMBS.txt — combinations of atoms that were used for calculations.</li> <li><PDB_ID>_alignment_X.pdb — original template that was aligned to the protein atoms. X denotes a number of the alignment.</li> <li><PDB_ID>_site_X.pdb — this pdb file contains eight atoms that form the site for K+ and which were used for the corresponding alignment X.</li> <li><PDB_ID>_RES.txt — the combinations of protein atoms that form the site are written in square brackets. The RMSD value for the alignment to this site is written to the right of them.</li> <li><PDB_ID>_RMSD.log — this file contains RMSD values of the template alignment to the corresponding site.</li> </ul>
Interaction of the inhibitory peptides ShK and HmK with the voltage-gated potassium channel KV1.3: Role of conformational dynamics
<p><strong>ABSTRACT: </strong>Peptide toxins that adopt the ShK fold can inhibit the voltage-gated potassium channel K<sub>V</sub>1.3 with IC<sub>50</sub> values in the pM range, and are therefore potential leads for drugs targeting autoimmune and neuroinflammatory diseases. NMR relaxation measurements and pressure-dependent NMR have shown that, despite being cross-linked by disulfide bonds, ShK itself is flexible in solution. This flexibility affects the local structure around the pharmacophore for K<sub>V</sub>1.3 channel blockade and, in particular, the relative orientation of the key Lys and Tyr side chains (Lys22 and Tyr23 in ShK), and has implications for the design of K<sub>V</sub>1.3 inhibitors. In this study, we have performed molecular dynamics (MD) simulations on ShK and a close homolog, HmK, in order to probe the conformational space occupied by the Lys and Tyr residues, and docked the different conformations with a recently determined cryo-EM structure of the K<sub>V</sub>1.3 channel. Although ShK and HmK have 60% sequence identity, their dynamic behaviors are quite different, with ShK sampling a broad range of conformations over the course of a 5 μs MD simulation, while HmK is relatively rigid. We also investigated the importance of conformational dynamics, in particular the distance between the side chains of the key dyad Lys22 and Tyr23, for binding to K<sub>V</sub>1.3. Although these peptides have quite different dynamics, the dyad in both adopts a similar configuration upon binding, revealing a conformational selection upon binding to K<sub>V</sub>1.3 in the case of ShK. Intriguingly, the more flexible peptide, ShK, binds with nearly 300-fold higher affinity than HmK.</p>
Conifer metabolite pisiferic acid restores activity in human Kv1.2 potassium channels carrying pathogenic sequence variants
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Vasorelaxant effects of 3-methoxycatechol are not via direct activation of voltage-gated potassium channels
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The potassium channel subunit Kv1.8 (Kcna10) is essential for the distinctive outwardly rectifying conductances of type I and II vestibular hair cells
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Polymodal potassium channel modulation contributes to dual analgesic and anti-inflammatory actions of ancient botanical medicines
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A novel autism-associated KCNB1 mutation dramatically slows Kv2.1 potassium channel gating activation, deactivation and inactivation
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Data from: Positive allosteric modulation of emodepside sensitive <em>Brugia malayi</em> SLO-1F and <em>Onchocerca volvulus</em> SLO-1A potassium channels by GoSlo-SR-5-69
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A selective small-molecule agonist of G protein-gated inwardly-rectifying potassium channels reduces epileptiform activity in a mouse model of tumor associated epilepsy - Part 2: WT Non-Tumor MEA Data
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Data from: Effects of emodepside on single-channel properties of <em>Onchocerca volvulus</em> SLO-1A (BK) potassium channels
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Optogenetic silencing by combining a rhodopsin cyclase with an engineered cGMP-gated potassium channel
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A selective small-molecule agonist of G protein-gated inwardly-rectifying potassium channels reduces epileptiform activity in a mouse model of tumor associated epilepsy - Part 3: Thy1-GCaMP Tumor Imaging EXCERPT
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The molecular basis of pH sensing by the human fungal pathogen Candida albicans TOK potassium channel
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.